getHRMF: Batch High Resolution Mass Filtering for all compounds in an...

In enviGCMS: GC/LC-MS Data Analysis for Environmental Science

Batch High Resolution Mass Filtering for all compounds in an MSP file

Description

Applies HRMF to every compound in an MSP file that has a chemical formula annotation.

Usage

getHRMF(
  file,
  charge = 1,
  adduct = NULL,
  mass_accuracy = 5,
  intensity_cutoff = 1,
  IR_RelAb_cutoff = 1
)

Arguments

file	character. Path to an MSP file.
charge	integer. Charge state (see HRMF). Default 1. Ignored when adduct is supplied.
adduct	character vector of adduct names or named numeric vector of custom mass deltas (see HRMF). Default NULL.
mass_accuracy	numeric. Mass accuracy in ppm. Default 5.
intensity_cutoff	numeric. Minimum absolute intensity. Default 1.
IR_RelAb_cutoff	numeric. Relative abundance cutoff (%) for theoretical isotopologues. Default 1.

Value

A named list where each element contains the HRMF results for one compound (with a valid formula) from the MSP file.

See Also

HRMF, getMSP

Examples

## Not run: 
results <- getHRMF("library.msp")

# LC-MS/MS library with protonated ions
results <- getHRMF("library.msp", adduct = "[M+H]+")

## End(Not run)

enviGCMS documentation built on Oct. 7, 2026, 5:07 p.m.